At a glance
This report contains visualisations of alignment statistics for paired tumor/normal samples that can help in understanding the results from wf-somatic-variation. Each section contains different plots or tables. You can quickly jump to an individual section with the links in the header bar.
Tumor Total Reads
1781909
Normal Total Reads
293794
Tumor Read N50
8349 bp
Normal Read N50
7094 bp
Tumor mean coverage
2.471x
Normal mean coverage
0.365x
Base statistics
The aligned bam files have been tested for coverage thresholds of 20.0x for the tumor and 20.0x for the normal sequences.
| Sample | Type | Total Reads | Median Read Length | Read N50 | Min chrom. coverage | Mean chrom. coverage | Max chrom. coverage | Pass threshold |
|---|---|---|---|---|---|---|---|---|
| SAMPLE | Tumor | 1781909 | 2316 | 8349 | 0.243 | 2.471 | 1068.097 | FAIL |
| SAMPLE | Normal | 293794 | 2149 | 7094 | 0.044 | 0.365 | 135.737 | FAIL |
Read statistics
| ref | sample_name | total | primary | secondary | supplementary | unmapped | qcfail | duplicate | duplex | duplex_forming | status |
|---|---|---|---|---|---|---|---|---|---|---|---|
| chr1 | SAMPLE | 203103 | 154718 | 47406 | 979 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr2 | SAMPLE | 164158 | 139228 | 24027 | 903 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr3 | SAMPLE | 170717 | 157546 | 12071 | 1100 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr4 | SAMPLE | 140735 | 97365 | 42338 | 1032 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr5 | SAMPLE | 138972 | 107662 | 30217 | 1093 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr6 | SAMPLE | 123550 | 112761 | 10163 | 626 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr7 | SAMPLE | 97158 | 83539 | 13013 | 606 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr8 | SAMPLE | 96925 | 86531 | 9875 | 519 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr9 | SAMPLE | 115621 | 81612 | 33272 | 737 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr10 | SAMPLE | 107110 | 80663 | 25806 | 641 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr11 | SAMPLE | 90289 | 79815 | 9937 | 537 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr12 | SAMPLE | 97465 | 91401 | 5498 | 566 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr13 | SAMPLE | 67726 | 62914 | 4497 | 315 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr14 | SAMPLE | 61391 | 56221 | 4847 | 323 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr15 | SAMPLE | 65749 | 50386 | 15011 | 352 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr16 | SAMPLE | 74332 | 53124 | 20551 | 657 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr17 | SAMPLE | 68847 | 47584 | 20842 | 421 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr18 | SAMPLE | 40179 | 34011 | 5918 | 250 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr19 | SAMPLE | 46646 | 31034 | 15255 | 357 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr20 | SAMPLE | 72287 | 50944 | 20814 | 529 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr21 | SAMPLE | 46345 | 25059 | 20927 | 359 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr22 | SAMPLE | 29474 | 17597 | 11311 | 566 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chrM | SAMPLE | 5966 | 4931 | 19 | 1016 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chrX | SAMPLE | 70922 | 61774 | 8709 | 439 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chrY | SAMPLE | 12716 | 2514 | 9838 | 364 | 0 | 0 | 0 | 0 | 0 | Mapped |
| * | SAMPLE | 10975 | 0 | 0 | 0 | 10975 | 0 | 0 | 0 | 0 | Unmapped |
| ref | sample_name | total | primary | secondary | supplementary | unmapped | qcfail | duplicate | duplex | duplex_forming | status |
|---|---|---|---|---|---|---|---|---|---|---|---|
| chr1 | SAMPLE | 36928 | 25488 | 11203 | 237 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr2 | SAMPLE | 27037 | 23772 | 3113 | 152 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr3 | SAMPLE | 19985 | 17330 | 2537 | 118 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr4 | SAMPLE | 19672 | 13352 | 6197 | 123 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr5 | SAMPLE | 24653 | 18196 | 6292 | 165 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr6 | SAMPLE | 22056 | 18964 | 2999 | 93 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr7 | SAMPLE | 22941 | 18974 | 3830 | 137 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr8 | SAMPLE | 12589 | 11035 | 1493 | 61 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr9 | SAMPLE | 19067 | 13036 | 5849 | 182 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr10 | SAMPLE | 17863 | 13885 | 3868 | 110 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr11 | SAMPLE | 16092 | 13657 | 2364 | 71 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr12 | SAMPLE | 17370 | 14662 | 2610 | 98 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr13 | SAMPLE | 9290 | 7675 | 1573 | 42 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr14 | SAMPLE | 10882 | 9065 | 1775 | 42 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr15 | SAMPLE | 7629 | 6064 | 1531 | 34 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr16 | SAMPLE | 12223 | 9154 | 3016 | 53 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr17 | SAMPLE | 15659 | 10874 | 4706 | 79 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr18 | SAMPLE | 9686 | 6942 | 2685 | 59 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr19 | SAMPLE | 11017 | 7013 | 3951 | 53 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr20 | SAMPLE | 13144 | 9409 | 3645 | 90 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr21 | SAMPLE | 8886 | 5094 | 3722 | 70 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chr22 | SAMPLE | 8133 | 4881 | 3133 | 119 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chrM | SAMPLE | 740 | 622 | 3 | 115 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chrX | SAMPLE | 11646 | 9603 | 1984 | 59 | 0 | 0 | 0 | 0 | 0 | Mapped |
| chrY | SAMPLE | 2562 | 556 | 1913 | 93 | 0 | 0 | 0 | 0 | 0 | Mapped |
| * | SAMPLE | 4491 | 0 | 0 | 0 | 4491 | 0 | 0 | 0 | 0 | Unmapped |
Coverage
Depth of coverage computed by mosdepth. The dashed line shows the total mean coverage.